Amino Acid Substitutions in Positions 385 and 393 of the Hydrophobic Region of VP4 May Be Associated with Rotavirus Attenuation and Cell Culture Adaptation
Abstract
:1. Introduction
2. Materials and Methods
2.1. Rotavirus Strains
2.2. Complete Genomic Sequencing of Human/Animal Group A Rotavirus Strains
2.3. Nucleotide and aa Sequences Analyze and Comparison
3. Results
3.1. Summary of the Total Nucleotide and aa Changes of Four RV Strains
3.2. Mutations Detected After Serial Passaging The RVA Strains in MA104 Cell Culture
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Primer Name | Sequence (5′→3′) |
---|---|
HRV-M-NSP4-F1 | GCGTGCGGAAAGATGGATAAG |
HRV-M-NSP4-R352 | CAATCATCTCCAGCTGACGTC |
HRV-M-NSP4-F258 | GGCTGGATATAAAGAGCAGGTTA |
HRV-M-NSP4-R697 | ATTAACGTCCAACACTCGCTG |
HRV-M-VP7-F1 | CGTTTGGCTAGCGGTTAGCT |
HRV-M-VP7-F309 | TGATAACTCATGGAAGGATACAC |
HRV-M-VP7-R664 | TTGTATCAGTAGTTAGACACCC |
HRV-M-VP7-R1023 | TAACCTAAGCTATATCTATACTCTG |
HRV-M-VP7-FOUT840 | AACAGCTGATCCAACGACAG |
HRV-M-VP7-ROUT178 | GTGCATCAAGGAGTGGTGAC |
PRV-OSU-VP4-F730 | GTGCACACAAGAGCTCAAGTTA |
PRV-OSU-VP4-F1067 | GGGATGATTCACAAGCATTCAG |
PRV-OSU-VP4-R1151 | CTACCACCAGTACACGTTACTG |
PRV-OSU-VP4-F1466 | CTGTGAGGCAAGATCTAGAGAG |
PRV-OSU-VP4-R1514 | AACTCATCTCGTAGCTCTCCC |
PRV-OSU-VP4-F1772 | GGACGGAAGTGTCAAATTCGATC |
PRV-OSU-VP4-R1867 | CTTTCAATCGTAACCGCTTAGC |
PRV-OSU-VP4-F1969 | CCGGAAATAGTTACTGAAGCTTC |
PRV-OSU-VP4-R2095 | CGAATGTGTCTACACGATATGCG |
PRV-OSU-VP4-R2336 | GGTCACAACTACTTACAGTCTAC |
Nucleotide/Amino Acid Substitutions | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Strain | VP4 | VP7 | NSP5 | VP3 | NSP1 | NSP4 | VP1 | VP2 | VP6 | NSP3 | NSP2 |
M | 10/8 | 1/1 | 0/0 | 2/2 | 0/0 | 0/0 | 0/0 | 0/0 | 3/3 | 0/0 | 0/0 |
Wa | 9/6 | 4/4 | 2/2 | 0/0 | 0/0 | 3/3 | 2/2 | 0/0 | 0/0 | 1/1 | 0/0 |
OSU | 8/7 | 0/0 | 0/0 | 0/0 | 0/0 | 0/0 | 0/0 | 0/0 | 0/0 | 0/0 | 0/0 |
Gottfried | 6/6 | 0/0 | 1/1 | 2/1 | 3/1 | 0/0 | 0/0 | 3/2 | 0/0 | 1/1 | 0/0 |
Total | 33/27 | 5/5 | 3/3 | 4/3 | 3/1 | 3/3 | 2/2 | 3/2 | 3/3 | 2/2 | 0/0 |
Nonsynonymous Substitution rate (%) a | 81.8 | 100 | 100 | 75 | 33.3 | 100 | 100 | 66.7 | 100 | 100 | 0 |
A | |||||
nt | |||||
Gene | aa | M | Wa | OSU | Gottfried |
VP4 | 24 | A→G | |||
8 | Gln | ||||
152 | G→T | ||||
51 | Gly→Val | ||||
230 | C→T | ||||
77 | Pro→Leu | ||||
235 | A→G | ||||
79 | Asn→Gly | ||||
236 | A→G | ||||
79 | Asn→Gly | ||||
391 | C→A | ||||
131 | Arg→Ser | ||||
434 | A→C | ||||
145 | Lys→Thr | ||||
503 | A→C | ||||
168 | Lys→Thr | ||||
532 | G→A | ||||
178 | Asp→Asn | ||||
554 | T→C | ||||
185 | Ile→Thr | ||||
559 | G→A | ||||
187 | Gly→Ser | ||||
582 | T→C | ||||
194 | Pro | ||||
613 | T→C | ||||
205 | Tyr→His | ||||
800 | A→G | ||||
267 | Tyr→Cys | ||||
992 | C→T | ||||
331 | Ser→Phe | ||||
1027 | G→T | ||||
343 | Val→Leu | ||||
1153 | G→A | G→A | G→A | ||
385 | Asp→Asn | Asp→Asn | Asp→Asn | ||
1177 | G→C | ||||
393 | Asp→His | ||||
1411 | T→C | ||||
471 | Ser→His | ||||
1412 | C→A | C→T | |||
471 | Ser→His | Ser→Leu | |||
1420 | C→T | ||||
474 | Pro→Ser | ||||
1572 (!) | A→T | ||||
524 (!) | Leu | ||||
1617 | A→G | ||||
539 | Leu | ||||
1761 | T→C | ||||
587 | Asp | ||||
1971 | C→T | ||||
657 | Asp | ||||
1997 | T→C | ||||
666 | Phe→Ser | ||||
2003 | C→T | ||||
668 | Pro→Leu | ||||
2029 | G→A | ||||
677 | Asp→Asn | ||||
2051 | C→T | ||||
684 | Asp→His | ||||
2137 | G→A | ||||
713 | Asp→Asn | ||||
B | |||||
nt | |||||
Gene | aa | M | Wa | OSU | Gottfried |
NSP1 | 1038 | T→C | |||
346 | Tyr | ||||
1074 | G→A | ||||
358 | Leu | ||||
1133 | C→T | ||||
378 | Thr→Met | ||||
NSP3 | 247 | G→T | |||
83 | Ala→Ser | ||||
859 | A→G | ||||
287 | Ile→Val | ||||
NSP4 | 131 | T→C | |||
50 | Val→Ala | ||||
59 | T→C | ||||
20 | Leu→Ser | ||||
113 | C→T | ||||
38 | Pro→Leu | ||||
NSP5 | 91 | T→C | |||
31 | Phe→Leu | ||||
143 | A→G | ||||
48 | Asn→Ser | ||||
209 | G→A | ||||
70 | Arg→Gln | ||||
VP1 | 1936 | G→A | |||
646 | Ala→Thr | ||||
3023 | G→A | ||||
1008 | Arg→Gln | ||||
VP2 | 1290 | G→A | |||
430 | Leu | ||||
1949 | C→T | ||||
650 | Ser→Leu | ||||
2623 | C→T | ||||
875 | Pro→Ser | ||||
VP3 | 282 | G→A | |||
94 | Met→Ile | ||||
794 | A→G | ||||
265 | Leu | ||||
2202 | G→A | ||||
734 | Met→Ile | ||||
2518 | G→A | ||||
Glu→Lys | |||||
VP6 | 169 | A→T | |||
57 | Ile→Val | ||||
475 | C→T | ||||
159 | Leu→Phe | ||||
1063 | G→A | ||||
355 | Ala→Thr | ||||
VP7 | 223 | A→C | |||
75 | Thr→Leu | ||||
224 | C→T | ||||
75 | Thr→Leu | ||||
293 | C→T | ||||
98 | Ala→Val | ||||
472 | G→A | ||||
158 | Glu→Lys | ||||
823 | T→C | ||||
275 | Ser→Pro | ||||
869 | C→T | ||||
290 | Thr→Ile |
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Guo, Y.; Wentworth, D.E.; Stucker, K.M.; Halpin, R.A.; Lam, H.C.; Marthaler, D.; Saif, L.J.; Vlasova, A.N. Amino Acid Substitutions in Positions 385 and 393 of the Hydrophobic Region of VP4 May Be Associated with Rotavirus Attenuation and Cell Culture Adaptation. Viruses 2020, 12, 408. https://doi.org/10.3390/v12040408
Guo Y, Wentworth DE, Stucker KM, Halpin RA, Lam HC, Marthaler D, Saif LJ, Vlasova AN. Amino Acid Substitutions in Positions 385 and 393 of the Hydrophobic Region of VP4 May Be Associated with Rotavirus Attenuation and Cell Culture Adaptation. Viruses. 2020; 12(4):408. https://doi.org/10.3390/v12040408
Chicago/Turabian StyleGuo, Yusheng, David E. Wentworth, Karla M. Stucker, Rebecca A. Halpin, Ham Ching Lam, Douglas Marthaler, Linda J. Saif, and Anastasia N. Vlasova. 2020. "Amino Acid Substitutions in Positions 385 and 393 of the Hydrophobic Region of VP4 May Be Associated with Rotavirus Attenuation and Cell Culture Adaptation" Viruses 12, no. 4: 408. https://doi.org/10.3390/v12040408